5O9I

Crystal structure of transcription factor IIB Mvu mini-intein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Basis for the Persistence of Homing Endonucleases in Transcription Factor IIB Inteins.

Iwai, H.Mikula, K.M.Oeemig, J.S.Zhou, D.Li, M.Wlodawer, A.

(2017) J. Mol. Biol. 429: 3942-3956

  • DOI: 10.1016/j.jmb.2017.10.016
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Inteins are mobile genetic elements that are spliced out of proteins after translation. Some inteins contain a homing endonuclease (HEN) responsible for their propagation. Hedgehog/INTein (HINT) domains catalyzing protein splicing and their nested HE ...

    Inteins are mobile genetic elements that are spliced out of proteins after translation. Some inteins contain a homing endonuclease (HEN) responsible for their propagation. Hedgehog/INTein (HINT) domains catalyzing protein splicing and their nested HEN domains are thought to be functionally independent because of the existence of functional mini-inteins without HEN domains. Despite the lack of obvious mutualism between HEN and HINT domains, HEN domains are persistently found at one specific site in inteins, indicating their potential functional role in protein splicing. Here we report crystal structures of inactive and active mini-inteins derived from inteins residing in the transcription factor IIB of Methanococcus jannaschii and Methanocaldococcus vulcanius, revealing a novel modified HINT fold that might provide new insights into the mutualism between the HEN and HINT domains. We propose an evolutionary model of inteins and a functional role of HEN domains in inteins.


    Organizational Affiliation

    Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, P.O. Box 65, Helsinki FIN-00014, Finland. Electronic address: hideo.iwai@helsinki.fi.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transcription initiation factor IIB,Transcription initiation factor IIB
A, B
195Methanocaldococcus vulcanius (strain ATCC 700851 / DSM 12094 / M7)Mutation(s): 0 
Gene Names: tfb
Find proteins for C9REA0 (Methanocaldococcus vulcanius (strain ATCC 700851 / DSM 12094 / M7))
Go to UniProtKB:  C9REA0
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.222 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 108.183α = 90.00
b = 67.245β = 102.43
c = 51.226γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
XDSdata reduction
MR-Rosettaphasing
XDSdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Academy of FinlandFinland1131413
Academy of FinlandFinland137995
National Cancer Institute, NIHUnited StatesHHSN261200800001E

Revision History 

  • Version 1.0: 2017-11-01
    Type: Initial release
  • Version 1.1: 2017-12-06
    Type: Database references